CN110327993B - Sequencing device - Google Patents

Abstract

The present invention relates to improvements in sequencing devices. Specifically, a system is disclosed that includes a cartridge manifold to connect to a cartridge and provide fluid communication between a plurality of reactant enclosures and a fluid circuit, and fluid communication between a compressed gas system, a cartridge cavity, and a scrubber of the cartridge; the fluid circuit; a sequencing device in fluid communication with the fluidic circuit; a pinch flow regulator in fluid communication with the sequencing device; and a waste container in fluid communication with the nip flow regulator.

Description

Sequencing device

This application is a divisional application of an invention patent application having an application number of 201580033060.6, an application date of 2015, 6/17, and an invention name of "sequencing apparatus".

Technical Field

The present invention relates generally to improved sequencing devices.

Background

Biological and medical research is increasingly turning to sequencing for enhanced biological research and medicine. For example, biologists and zoologists are turning to sequencing to study the migration of animals, the evolution of substances, and the source of characteristics. The medical community turned to sequencing for studying the cause of disease, sensitivity to drugs, and the cause of infection. Sequencing has historically been an expensive task, thus limiting its implementation.

Drawings

The present invention may be better understood, and its numerous features and advantages made apparent to those skilled in the art by referencing the accompanying drawings.

Fig. 1 includes an illustration of an example sequencing instrument.

Fig. 2 contains a schematic of an example sequencing instrument.

Fig. 3 includes a schematic of an example sequencing instrument.

FIG. 4 is a perspective view depicting an exemplary reactant storage device.

FIG. 5 is a perspective view illustrating an example container.

FIG. 6 is a cross-sectional perspective view depicting an example container.

FIG. 7 is an exploded schematic view depicting an example container.

FIG. 8 is a detailed perspective view illustrating an example container.

FIG. 9 is a perspective view depicting an exemplary reactant storage device.

FIG. 10 is a perspective view illustrating an example container.

FIG. 11 is a cross-sectional perspective view depicting an example container.

Fig. 12, 13, 14, 15, and 16 include illustrations of exemplary pockets for enclosing one or more enclosures.

Fig. 17 and 18 illustrate schematic diagrams of example methods.

FIG. 19 is an exploded schematic view depicting an example valve.

FIG. 20 is a schematic cross-sectional view depicting an example valve.

FIG. 21 is a schematic cross-sectional view depicting an example valve.

FIG. 22 is a schematic cross-sectional view depicting an example valve.

Fig. 23 and 24 include illustrations of example manifolds and cassettes.

Fig. 25 includes an illustration of an example fluid circuit.

Fig. 26 includes a flow diagram of an example method for preparing a reactant solution.

Fig. 27 includes a flow diagram of an example method for measuring an analyte.

FIG. 28 includes a flow diagram of an example method for preparing a reagent cartridge.

The use of the same reference symbols in different drawings indicates similar or identical items.

Detailed Description

In an exemplary embodiment, a sequencing system includes an instrument to receive a semiconductor sequencing chip and to perform a process of generating an identification of a base sequence. In particular, the instrument can receive a reagent cartridge, a wash solution, and a semiconductor sequencing chip. The instrument may include a user interface, such as a touch screen user interface, and may include computing circuitry and a controller to control delivery of reagents and wash solutions to a semiconductor sequencing chip, as well as acquisition of data from a semiconductor sequencing chip to facilitate identification of the substrate sequence.

An exemplary instrument includes a reagent cartridge receptacle, another receptacle for receiving a wash buffer cartridge, and a chip gripper for receiving a semiconductor sequencing chip. Further, the instrument includes a touch screen user interface. This instrument provides limited sequencer touch points, no compressed gas utilization (actually utilizing a closed pump-driven system), no high quality water utilization, easy operation (including intuitive graphical user interfaces, plug-and-play consumer products, etc.), fast single-day run time, integrated on-board computing for primary data analysis, dual mode operation in research-only (RUO) or diagnostic mode (Dx), small desktop footprint, scalability (scalable chassis for different performance levels), or low cost, or any combination thereof.

In particular, the instrument may include a compressor for providing an internally generated gas pressure. The reagent may be provided in a pre-loaded cartridge to limit user interaction with the reagent preparation. Similarly, the cleaning solution can be provided, for example, within the cartridge as a plug-and-play cleaning solution. In one example, the pH of the wash solution may be stabilized using a solid buffer.

The flow rate of reactants within the system may be controlled using pinch valve regulators, for example, using dynamic flow control. The system may also include a cleaning solution that performs an automatic post-run wash. The apparatus may include an internal server for processing data received from a semiconductor sequencing chip. Alternatively or additionally, the system may provide an output data port to connect to an external server for processing data. Further, the internal computing system may be configurable and upgradeable.

The system can use an internal gas supply to drive the liquid flow with pressure, and not an external gas supply. In particular, the reagent cartridge system can utilize liquid or lyophilized nucleotides in a separate enclosure or bag. Any initial air content within the enclosure can be vented by pressurizing a chamber outside the bag and letting air from the bag flow out as waste. The cleaning solution may be applied to the bag. Residual bubbles can rise to the top and can be purged out as waste. Mixing is achieved by pressurizing and rapidly depressurizing a chamber outside the bag, thereby causing pressurization and depressurization of the liquid in the bag. The liquid or lyophilized nucleotide is contained within a mixer (reagent container) that discharges a solution containing the nucleotide in response to reduced pressure, thereby causing mixing of the nucleotide within the bag.

As external gas pressure is applied to the bag enclosure, the internal cleaning solution flows into the mixer and the internal compressible volume within the mixer compresses. When the gas pressure outside the bag is rapidly released, the pressure of the filling in the compressible volume forces the wash solution out through the nozzle at a high velocity, thereby mixing the nucleotide-containing liquid in the bag.

When a flow is applied through a flow cell of a semiconductor sequencing chip, dynamic flow control can be achieved by utilizing a pinch flow regulator (pinch valve regulator). This dynamic flow control reduces the use of resistive tubing coils and reduces the likelihood of plugging. The flow rate may be programmable and may be adjusted by adjusting a control pressure within the pinch flow regulator.

The system may utilize a solid buffer system, such as a ceramic buffer system (e.g., particulate titanium dioxide). The wash solution reactants can be provided in a single use bottle that is easily mixed. The solution may compriseSolid buffer, eliminates the automatic pH routine, and provides long-term pH stability. The particulate titanium dioxide can be easily confined to the bottle by the filter, thus confining the particles within the system. Furthermore, the primary wash bottle may utilize a cleaning solution having a low permeability to gases and thus to acidified CO₂Low permeability encapsulation. The container may also be CO-fed₂The absorbent packets are shipped together to further limit exposure to carbon dioxide.

The semiconductor sequencing chip may be received in a chip holder that loads the chip in the system and connects the chip to the fluidic system. The chip gripper may include an integrated squid valve manifold and remove the plumbing connections. The chip holder may further include a reference electrode, integrated chip temperature control, and integrated manifold heating.

The instrument may further rely on reagent cartridges, limiting user access and handling. A simple cassette is loaded and it contains five containers or enclosures (for nucleotide and bead search or pH adjustment reagents). The cartridge may also include a fill port to rapidly pressurize/depressurize the cartridge with, for example, a vent valve connected to a manifold of the reactant cartridge. Optionally, a static bar is applied to the vent to reduce noise associated with rapid depressurization of the cartridge.

The instrument further includes scalable and configurable electronics. In particular, computing power and memory may be swapped. The system may further include support for RFID tags on, for example, semiconductor sequencing chips or cassettes.

An exemplary reagent cartridge may include color coding ports for different nucleotide solutions and bead-finding or pH-adjusting solutions. In addition, the reactant cartridge can be included for CO₂Input and output ports of the scrubber. The cartridge may also be provided with an RFID tag that identifies, for example, a lot number and an expiration date.

The cartridge may include a reactant container applied to or CO₂The individual chamber into which the washer is inserted. The reactant container is inserted via the cartridge lid into a reactant pouch or enclosure secured to the lid within the cartridge.

For exemplary reagent cartridge manufacturing, a fitment is applied to the bag, such as including a low density polyethylene/polyethylene terephthalate film. The cartridge base, lid, port gasket and other parts are then assembled: applying the pouch to the closure, subsequently applying the closure to the base, and inserting the gasket into the closure. The reactant reservoir contains a mixer body into which the foam member is inserted. A mixer cap is applied to the mixer body. In an example, the mixer cap can include a lyophilized reactant or a liquid reactant. In another example, the reactants may be frozen or stored within a porous ceramic or polymeric foam. The assembled reactant mixer and scrubber can then be applied to the reactant cartridge assembly. An RFID tag can be applied to the cartridge, and the cartridge can be boxed and stored for shipment.

The reagents may be applied to the mixer or cartridge in lyophilized form or in frozen liquid form. In one example, a lyophilized nucleotide pellet can be formed and then inserted into a mixer. In another example, the nucleotides may be dried onto filter paper integrated into a "worm" (bug) mixer. In another example, the nucleotide may be dried directly onto the compressible foam or into the closure (second portion) of the mixer (reagent container).

In one example, fig. 1 includes an illustration of an exemplary instrument 100 for sequencing. The instrument 100 can include a connector to receive a container of buffer solution 104, a clamp 106 to receive a sequencing device, and a manifold to receive a reagent cartridge 102. In addition, the sequencing instrument 100 includes computational circuitry to control fluid flow, data retrieval from the sequencing device, interpretation of the data, and a user interface 108. In a particular example, the sequencing device is a pH or ion sensitive device, e.g., comprising a plurality of Ion Sensitive Field Effect Transistors (ISFETs).

In a particular example, a sequencing instrument includes circuitry to control fluid flow within a system. In an example illustrated in fig. 2, the instrument 200 includes a connection to a cartridge 202. The reagents can flow from the cartridge 202 to the sequencing device 206 via the fluidic circuit 204. Fluid passing through the fluidic circuit 204 may optionally be directed to a waste container 212 or through a pinch flow regulator 208 or 230 via the sequencing device 206 to a waste container 210. In an alternative example, a single waste container may replace waste containers 210 or 212. An exemplary embodiment of the cartridge 202 is illustrated in FIGS. 12-16. Fig. 19-22 illustrate exemplary embodiments of pinch flow regulators. Exemplary fluid circuits are illustrated in fig. 3 and 25.

As described further below, a solution (e.g., a buffer solution) in the container 226 may flow through the valve 228 and be used to prepare the reactant solution in the reactant enclosure 214. The reagent solution 214 may selectively flow to the fluidic circuit 204 and to the sequencing device 206 or the waste containers 210 or 212. The solution in solution container 226 may optionally flow through valve 232 to fluidic circuit 204 and may act as a wash solution, washing fluidic circuit 204 and sequencing device 206 of reagents optionally from a reagent solution. The buffer solution in the solution container 226 may optionally be pumped through the system. Alternatively, the buffer solution may be driven by pressure supplied through inlet 234, for example, using air.

In an example, the system 200 can include a compressor 216 that compresses gas or air to flow through a scrubber cartridge 220 optionally included in the reagent cartridge 202. For example, the scrubber cartridge 220 may include a component such as soda lime to remove carbon dioxide from the air. The receptacle 218 may be used to store and supply pressurized air to the system. For example, pressurized air may be used to pressurize the solution container 226. In another example, pressurized air can be supplied to the cavity of the cartridge 202 to pressurize the reactant enclosure 214 and selectively drive the reactant solution to the fluidic circuit 204 via the valve 222. In another example, compressed air from the receptacle 218 may be used to clean the fluid circuit 204 via the valve 224. The pressurized air may drive the remaining liquid within the fluidic circuit 204 to the waste container 212, to the waste container 210 via the sequencing device 206, or back to the reactant enclosure 214 via the valve 222.

Fig. 3 includes an illustration of a more detailed embodiment of the fluid circuit. Fig. 3 illustrates a system employing an enclosure 614, the enclosure 614 being, for example, a reservoir of reactants for performing pH-based nucleic acid sequencing. Each electronic sensor of the device generates an output signal. The fluidic circuit permits delivery of a plurality of reactants to the reaction chamber.

In fig. 3, the system includes a fluidic circuit 602 connected to the reactant reservoir 614, to the waste reservoir 620, and to a biosensor 634 through a fluidic path 632, the fluidic path 632 connecting the fluidic node 630 to an inlet 638 of the biosensor 634 for fluid communication. The prepared and mixed reactant solution from reservoir 614 may be driven to fluid circuit 602 by a variety of methods, including pressure, pump (e.g., syringe pump), gravity feed, etc., and selected by control of valve 650. The reactants from the fluidic circuit 602 may be driven to the waste containers 620 and 636. The control system 618 includes a controller for the valve 650 that generates signals for opening and closing via the electrical connection 616.

The control system 618 also includes a controller for the other components of the system, such as a cleaning solution valve 624, which is connected thereto by an electrical connection 622, and a reference electrode 628. The control system 618 may also include control and data acquisition functions for the biosensor 634. In one mode of operation, the fluid circuit 602 delivers a selected sequence of reactants 1, 2, 3, 4, or 5 to the biosensor 634 under programmed control of the control system 618, such that between flows of selected reactants, the fluid circuit 602 is pre-charged and purged with the purge solution 626 and the biosensor 634 is purged with the purge solution 626. Fluid entering the biosensor 634 exits via the outlet 640 and is deposited in the waste container 636. A similar arrangement may be used for optical sequencing systems having, for example, photodiodes or CCD cameras.

In a particular example, the wash solution 626 can be a buffered suspension including solid buffer particles. The buffer suspension (wash solution) may be filtered using filter 660 before entering fluid circuit 602 or sensor 634. In another example, the buffered suspension may be applied to the reactant reservoir 614 via a filter 662 to form a reactant solution from a reactant concentrate within the reactant reservoir. Alternatively, filters 660 and 662 may be the same filter. In one example, the reactant concentrate is a liquid concentrate. In another example, the reactant concentrate is a dry concentrate, such as a lyophilized reactant (e.g., lyophilized nucleotide). Alternatively, the illustrated filters 660 and 662 may be combined. In another example, the filter may be located downstream of the reactant reservoir 614, such as between the reactant reservoir 614 and the valve 650.

Fig. 4 is a perspective view depicting an exemplary reactant storage apparatus 1100. In one example, reactant storage apparatus 100 can include enclosure 1110. The container 1120 is disposed within the enclosure 1110. In an example, the enclosure 1110 can be a flexible enclosure. The flexible enclosure (e.g., a sealable flexible bag enclosure) may be pressurized and depressurized by applying pressure externally (e.g., by applying pressurized gas to an outer surface of the flexible enclosure). Alternatively, the enclosure may be rigid such that externally applied gas pressure does not readily translate to the pressure of the fluid within enclosure 1110.

The reactant storage apparatus 1100 can also include a fluid port 1130 coupled to a fitting 1160 attached to the enclosure 1110 to provide fluid access to the interior of the enclosure 1110. The fluid port 1130 may be coupled to the fitting 1160 to seal the enclosure 1110 from the external environment after insertion of the container 1120. Enclosure 1110 may be, for example, thermoelectrically sealed to itself and to fitting 1160, except where otherwise sealed by fluid port 1130.

The container 1120 may include one or more arms 1140 and a flange 1150. The arms 1140 may position the container 1120 within the enclosure 1110, e.g., substantially centered, to provide for uniform dispersion of the reactants within the enclosure 1100. A flange 1150 may be provided to enable convenient assembly of the container 1120. In one example, the arms 1140 are flexible. For example, the arm 1140 may be formed of a wire or a polymeric material. Alternatively, the arms 1140 may be rigid. Alternatively, the arms 1140 and flanges 1150 are not limited to those illustrated in fig. 4 and may include structure to position the container in a predetermined position or orientation within the enclosure 1110. Container 1120 may be directly or indirectly connected to fluid port 1130, or positioned a suitable distance from fluid port 1130 (as shown in fig. 4). Sealed enclosure 1100, which includes enclosure 1110 and container 1120, provides simplified storage and transport of the reactants within container 1120.

FIG. 5 is a perspective view illustrating an example vessel 1200. The container 1200 may include a first portion 1210 and a second portion 1220 coupled to the first portion 1210. Elements such as optional compressible members and reagents may be inserted within the vessel 1200 prior to connecting the first portion 1210 to the second portion 1220. In an example, the second portion 1220 can be a cap that slides over or otherwise covers a portion of the first portion 1210 to form an internal cavity. In another example, the second portion 1220 can be an insert that slides into the first portion 1210. The second portion 1220 can be connected to the first portion 1210 by any suitable attachment mechanism, including screwing the second portion 1220 onto the first portion 1210 or vice versa, a locking mechanism, an adhesive, or any other suitable attachment mechanism.

In an example, the internal cavity defines a compressible volume. The compressible volume compresses in response to fluid pressure and does not dissipate or exit the internal cavity of the vessel 1200. The compressible volume may comprise a compressible gas volume or may be a compressible member, such as an elastomeric polymer or foam.

The vessel 1200 may define a passage 1230, providing fluid communication between an interior cavity of the vessel 1200 and an exterior of the vessel 1200. In an example, one or more passageways 1230 can be defined through to the interior cavity. Such passages 1230 may be drilled through the first or second portions of the vessel 1200. In another example, the second portion 1220 can include the passage 1230 or can include a slit that extends beyond the region where the second portion 1220 engages the first portion 1210, thus forming the passage 1230.

One or more arms 1240 may be coupled to the first portion 1210 to position the container 1200 within the enclosure as desired. A flange 1250 may be coupled to the second portion 1220 to assist in applying the second portion 1220 to the first portion 1210 or to position the container 1200 away from the bottom of the enclosure.

Fig. 6 is a cross-sectional perspective view depicting an example container 1300. The container 1300 defines an interior cavity 1320 and defines a passage 1330 providing fluid communication between the interior cavity 1320 and the exterior of the container 1300. The passage 1330 may be drilled through the container 1300. In another example, the cap or insert may include a slit that extends beyond the region that engages the container 1300 and forms the passage 1330. The container 1300 may include a first portion 1310 and a second portion 1350 coupled to the first portion 1310, which allows elements such as the compressible member 1340 and reagents to be inserted into the internal cavity 1320 of the container 1300.

The internal cavity 1320 defines a compressible volume. A compressible volume is a volume that compresses in response to a pressure to match the pressure, and may expand in response to a reduced pressure, providing a reaction force against the fluid pressure. In an example, the compressible volume includes a compressible gas that compresses to match the pressure of the fluid entering the interior volume without dissipating or exiting the interior cavity, and pushes the fluid out of the interior cavity 1320 in response to the decompression of the fluid. Optionally, the compressible volume may contain a compressible member 1340. The compressible member 1340 can compress under pressure and substantially return to its previous shape after decompression. For example, the compressible member 1340 can be a foam material. In particular, the compressible member 1340 can be a closed cell foam of resilient material. In one example, the compressible member may comprise polyurethane foam.

In one example, a reactant can be disposed within the second portion 1350. The reactant may be a lyophilized nucleotide or an analog thereof. In another example, the reactant is a solution absorbed on a porous metal, ceramic, or polymeric sponge-like material or frit. Optionally, the reactant solution may be frozen. In alternative examples, the reactant may comprise a pH adjusting reactant, such as an acid or a base.

One or more arms 1360 may be coupled to the first portion 1310 to position the container 1300 within the enclosure as desired. A flange 1370 or other suitable accessory may be coupled to the second portion 1350 to assist in engaging the second portion 1350 with the first portion 1310 or positioning the container 1300 within the enclosure.

Fig. 7 is an exploded schematic diagram depicting an example container 1400. Container 1400 may include a first portion 1410 and a second portion 1420 (e.g., an insert) coupled to first portion 1410, allowing elements such as an optionally compressible member 1430 to be inserted within container 1400. Second portion 1420 may be secured to first portion 1410 by sliding or screwing to first portion 1410. One or more flexible arms 1440 may be coupled to the first portion 1410 to position the container 1400 within the enclosure. A flange 1450 may be coupled to second portion 1420 to assist in engaging second portion 1420 with first portion 1410 or positioning container 1400 within the enclosure.

In an example, the second portion 1420 may define one or more slits 1460. The first portion 1410 and the second portion 1420 can be joined so as to leave a portion of the one or more gaps 1460 exposed, thereby providing one or more passageways between the interior cavity of the container 1400 and the exterior of the container 1400.

FIG. 8 is a detailed perspective view illustrating an example container 1500. A detailed view of the container 1500 may define a passageway 1510 that provides fluid communication between the interior cavity of the container 1500 and the exterior of the container 1500. The end of the container 1500 includes a fitting 1530 to receive an insert 1540. The insert 1540 includes a hole or gap that is not covered when the insert 1540 is applied to the fitting, thereby forming the passage 1510. Alternatively, the insert 1540 may include holes, notches, screens, apertures, or any other suitable feature for providing fluid communication to the fitting 1530. The flange 1520 may be coupled to the container 1500 to allow control of the insert 1540 as the insert 1540 is applied to the fitting 1530 and to position the container within the enclosure.

Fig. 9 is a perspective view depicting an exemplary reactant storage apparatus 1600. Reactant storage apparatus 1600 includes an enclosure 1610. A container 1620 is disposed within enclosure 1610. The enclosure 1610 may be a flexible enclosure as described above. For example, the flexible enclosure may be a sealable flexible pouch enclosure that can be pressurized and depressurized externally via fluid or gas pressure. Alternatively, enclosure 1610 may be a rigid enclosure. Enclosure 1610 may sealingly engage a seal structure 1670, such as a fitting, having an aperture 1680 (e.g., a central aperture). Container 1620 may be coupled to arm 1640, which arm 1640 may be coupled to fluid port 1630 and inserted through aperture 1680 of fitting 1670.

Fluid port 1630 provides fluid access to the interior of enclosure 1610 via aperture 1680. Fluid port 1630 may be coupled to a seal structure or fitting 1670 of reagent storage device 1600 from the external environment after insertion into container 1620. Arm 1640 couples container 1620 to fluid port 1630 to generally center container 1620, for example, within enclosure 1610 to evenly disperse reactants within enclosure 1610. Arm 1640, container 1620, and fluid port 1630 may be a single integrated piece. In an example, fluid flows through fluid port 1630 and through aperture 1680 of fitting 1670 into enclosure 1610 (optionally along arms 1640). The arm 1640 may position the container 1620 with or without the flange 1650.

FIG. 10 is a perspective view illustrating an example container 1700. The container 1700 can include a first portion 1710 and a second portion 1720 coupled to the first portion 1710, thereby allowing elements such as an optional compressible member to be inserted within the container 1700. The fluid port 1730 is coupled to the container 1700 and provides fluid access to the enclosure into which the container 1700 is inserted. The arm 1740 may couple the first portion 1710 and the fluid port 1730 to position the container 1700 within the enclosure.

In one example, second portion 1720 is an insert to engage first portion 1710. In another example, second portion 1720 forms a cap to cover an end of first portion 1710. Fluid may flow through the opening 1770 of the port 1730 and along the arm 1740 to the opening 1760. The fluid port may include a gasket to facilitate sealing. The flange 1750 can be coupled to the second portion 1720.

FIG. 11 is a cross-sectional perspective view that illustrates an example container 1800. The container 1800 defines an interior cavity 1820 and defines a passageway 1830 providing fluid communication between the interior cavity 1820 and the exterior of the container 1800. The container 1800 may include a first portion 1810 and a second portion 1850 coupled to the first portion 1810, thereby defining a compressible volume. In an example, elements such as compressible member 1840 and a reactant can be inserted into interior cavity 1820 of container 1800.

In one example, the second portion 1850 is a cap to be applied over the end of the first portion 1810. In another example, the second portion 1850 is an insert to apply to the fitment of the first portion 1810. In an example, the passage 1830 is formed in the second portion 1850, e.g., as a hole or a slit.

A reactant can be disposed within the second portion 1850. The reactant may be a lyophilized nucleotide or an analog thereof. In another example, the reactant may be a solution of nucleotides absorbed by a porous metal, ceramic or polymeric sponge or frit. In another example, the reactants may be frozen. In another example, the reactant may comprise a pH-adjusting reactant, such as an acid or a base.

Fluid port 1860 is coupled to container 1800 and provides fluid access to the enclosure in which container 1800 is inserted. For example, fluid entering opening 1890 may pass through passage 1895 and into the enclosure. The arm 1870 may be coupled to the first portion 1810 and the fluid port 1860. A flange 1880 may be coupled to the second portion 1850 to also position the container 1800 within the enclosure.

The reagent storage device may be inserted into a middle box or cassette having a cavity. In an example, the pressure may be varied within the cavity to change the pressure of the liquid within the flexible enclosure and, thus, affect the pressure within the container. Alternatively, pressure may be applied through opening 1890 and inside the enclosure. In an example, one or more of the enclosures can be incorporated into a case. The tank may define one or more pressure chambers in which pressure may be applied and relieved from the enclosure.

In the particular example illustrated in fig. 12, a cartridge or case 1900 includes a lid 1902 and a body 1904. The closure 1902 may receive a fluid port (1906, 1908, 1910, 1912, or 1914) of a container inserted into the flexible enclosure. The containers may contain different reactants. For example, each container may comprise nucleotides or may comprise a pH-adjusting reagent. The enclosure 1902 may also include ports 1916 for providing pressurized gas or relieving pressure, controlling the pressure outside each of the enclosures and thereby controlling the pressure within the enclosures. The walls of the base 1904 and the lid 1902 can be configured to permit pressurization of a cavity within the cartridge 1900, for example, with a pressurized gas or air. In an example, the cartridge 1900 can be labeled with a barcode or a Radio Frequency Identification (RFID) tag.

As illustrated in fig. 12 and 13, the lid 1902 may include access ports 1918 and 1920 for applying gas or air via the scrubber cassette. In particular, the system may utilize outside air, applied via port 1918 and receiving clean gas or air via port 1920. In particular, the scrubber cartridge may include an absorbent material for capturing carbon dioxide or water. Carbon dioxide may be removed from the air to prevent acidification of the liquid component when the carbon dioxide diffuses into the enclosure or when air is used in other parts of the system.

In another example, the cover 1902 may also include an alignment feature 1924 or 1926. Such alignment features may be used to align access to the ports (1906, 1908, 1910, 1912, 1914, 1916, 1918, or 1920) with the manifold to limit damage to the manifold or to enable proper engagement between the manifold and the tank 1900.

As illustrated in fig. 14, 15, and 16, the body 1904 can define individual cavities 2126 in which each enclosure 2128 and the inserted nucleotide container 2130 are disposed. In an example, each enclosure 2128 is disposed within an individual cavity 2126, and each container 2130 is applied through the cap 1902, engaging the cap 1902 at a fluid port of the container 2130. The fitting 2134 of the enclosure 2128 can engage the cap 1902.

The cover 1902 may define a headspace that provides communication between the pressurized gas input port 1916 and each of the cavities 2126. Alternatively, the cavity may be an open cavity (without an individualized cavity 2126) and provide a single cavity into which pressurized gas may be applied to apply pressure to the enclosure 2128. As illustrated in fig. 15, the body 1904 may include a chamber 2232 to receive scrubber boxes, for example, for removing carbon dioxide from air.

In a top view, as illustrated in fig. 16, the body 1904 includes an individualized cavity 2126. In addition, the body may include a seal structure 2340 to isolate the scrubber cartridge input and output from the pressure of the rest of the body 1904. Additionally, the input pressure of air entering the scrubber box may be isolated from the output pressure of air exiting the scrubber box by an internal seal 2342. Further, the body 1904 may include a seal structure 2344 to engage an opposing seal structure on the cover 1902 to provide an isolated interior space including a cavity that may be pressurized or depressurized.

The container may contain nucleotide or other reactants. In particular, individual containers within a cartridge system can comprise one of four nucleotides. The system may also include a container within the enclosure containing the pH-adjusting reagent. In a particular example, a cartridge includes a container and an enclosure that incorporate each of four nucleotides (A, G, C or T), and optionally a pH-adjusted reactant container. In one example, the reactants are in dry form. For example, lyophilized nucleotides can be stored in a container. In another example, the reactant solution may be absorbed within a porous metal, ceramic, or polymeric sponge-like material or frit. In another example, the reactant solution may be frozen within a container or within a porous sponge-like material into which the reactant solution is absorbed.

The enclosures described herein may be used to prepare reactant solutions. Assembly of the enclosure includes inserting the container into the enclosure and sealing the container within the enclosure with the fluid port. One or more enclosures may further be secured to a volume of the tank, wherein the tank includes a gas port for providing external gas pressure to the secured enclosures. The enclosure may be inserted into the tank as a final assembly step or at a point just prior to mixing, which provides flexibility in the choice of reactants.

Alternatively, the enclosure may be secured to the lid prior to insertion of the container containing the reagent. The reagent container may be inserted through the closure and the fluid port of the container may engage the closure. The lid may be secured to the base after securing the enclosure to the lid or after inserting the container into the enclosure via the lid.

The pressurization and depressurization of the fluid within the enclosure is controlled by increasing and decreasing the gas pressure of the tank volume via the gas ports.

A method for preparing a reactant solution includes filling an enclosure (such as any of the enclosures described herein) with a predetermined amount of fluid via a fluid port of the enclosure (including a container and a reactant). The fluid within the enclosure is then pressurized such that the fluid flows into the interior cavity of the container via the passageway of the container. The fluid may be pressurized directly via the port. In another example, the fluid may be pressurized by applying external pressure to the enclosure, for example, using a gas or other fluid pressure. The pressurization compresses a compressible volume or component within the internal cavity of the container while the fluid fills a portion of the volume of the internal cavity.

For example, the fluid flows into the interior cavity of the container and compresses the compressible volume or member until the pressure within the interior cavity and exerted on the compressible volume or member is substantially equal to the pressure within the enclosure and outside the container.

After the predetermined pressure is reached, the fluid within the enclosure is depressurized. The compressible volume or member decompresses to expand and expel the fluid and reactant from the internal chamber into the enclosure outside the container. The mixture of reactant and fluid ejected from the passageway creates eddy currents and turbulence within the bag enclosure sufficient to mix the reactant with the fluid. After depressurization, the pressure within the internal cavity, as imposed by the compressible volume or component, is greater than the pressure within the enclosure and outside the container. The fluid and the reactant are ejected from the internal chamber via the passageway until the pressure within the internal chamber is approximately equal to the pressure within the enclosure and outside the container to provide a well-mixed reactant solution.

The pressurization may be performed by increasing the gas pressure outside the flexible enclosure. In one embodiment, the enclosure may be disposed within the tank. The pressure inside the enclosure can be controlled by increasing/decreasing the gas pressure inside the enclosure and outside the enclosure. Proper mixing of the reactants and fluids can be achieved via repeated cycles of pressurization and depressurization. After mixing is complete, the fluid and the reagent are released via the fluid port of the enclosure.

Fig. 17 and 18 illustrate an exemplary method for assembling a reagent cartridge. For example, fitment 702 may be secured to enclosure 708 in the form of a bag enclosure. A plurality of enclosures 708 can be coupled to the lid 706 of the cartridge and inserted into the cartridge base 704 as illustrated at 714 when the cartridge lid 706 is secured to the cartridge base 704. A port gasket 710 can be secured to the cassette lid to permit the compressed air system to connect to the cassette. In another example, port gasket 712 can be secured to cartridge lid 706 to permit access to the CO₂Access of the scrubber.

Turning to fig. 18, the reactant reservoir can be formed by inserting an optional compressible member into the first portion 716 of the reactant reservoir, as illustrated at 722. The second member 718 can be secured to the first portion 716 to form a reactant reservoir 728. Optionally, a reagent is applied to the second part 718. Alternatively, a reactant is inserted into the first portion at 722.

Scrubber vessel 720 may be filled with scrubbing reactants to remove CO₂For example, as illustrated at 726. The plurality of reactant containers 728 and the scrubber container 720 can be inserted into the reactant cartridge via the lid, as illustrated at 730. The end of the reactant cartridge container 728 is fed through the cartridge lid and into the interior of the reactant enclosure. The scrubber container 720 is inserted through the lid and into the isolated compartment of the cartridge, which permits air to flow in and out without affecting the pressure in the remaining cavity of the cartridge. A fluid port gasket 724 is secured over the reactant reservoir and optionally the scrubber reservoir to provide fluid-tight access to the reactant reservoir or scrubber reservoir when secured within the manifold and instrument.

FIG. 19 provides an exploded schematic view of an example pinch valve adjuster 3100. The valve 3100 includes a housing base 3110 and a housing cover 3120 disposed over the base 3110. The diaphragm 3130 is disposed between the housing base 3110 and the housing cover 3120. A pinch plate 3140 is disposed between the diaphragm 3130 and the base 3110. In operation, the pinch plate 3140 moves relative to the housing base 3110 to pinch the pinch tube 3150 against a pinch structure (as more clearly illustrated in fig. 20, 21, and 22) to restrict fluid flow through the pinch tube 3150. One or more gaskets 3160, 3170 may be disposed between the housing base 3110 and the housing cover 3120 to prevent fluid leakage and ensure smooth valve operation.

FIG. 20 provides a schematic cross-sectional view of an example pinch valve adjuster. The valve 3200 includes a housing base 3210 and a housing cover 3220 disposed over the base 3210. The housing base 3210 includes a lower cavity 3212 and pinch structures 3214 protruding within the lower cavity 3212. The housing base 3210 includes a gas inlet 3230, providing access to the lower cavity 3212 from the outside. The base fluid inlet 3232 provides an external access path that connects to an end of a pinch tube 3240 within the lower cavity 3212. The other end of the pinch tube 3240 is connected to a substrate fluid outlet 3234. Thus, the pinch tube 3240 provides fluid communication between the base fluid inlet 3232 and the base fluid outlet 3234. The pinch tube 3240 extends between the pinch structure 3214 and a pinch point 3252 of the pinch plate 3250.

In an example, the pinch structures 3214 include rectangular prisms extending into the lower cavity 3212. As illustrated, the rectangular prism has a domed portion. In another example, a rectangular prism may have a flat top. Alternatively, the prisms may have a pointed structure, for example, triangular prisms. Generally, the pinch structures 3214 form counter structures to which pinch points 3252 can secure and perforate the pinch tube 3240.

The base fluid outlet 3234 is in turn connected to a lid fluid inlet 3236 between the upper and lower cavities and provides fluid communication with the lid fluid inlet 3236 to provide a fluid path through the housing base 3210 and housing lid 3220. Cap fluid inlet 3236 is in fluid communication with cap fluid outlet 3238 via fluid path 3270. Cover fluid outlet 3238 provides external access to fluid path 3270 from housing cover 3220. The septum 3260 is disposed between the housing base 3210 and the housing cover 3220 to fluidly separate the lower cavity 3212 from the upper cavity 3222 defined between the cover 3220 and the septum 3260.

Housing cover 3220 defines an upper cavity 3222 in which fluid path 3270 is disposed. Optionally, the gasket 3280 can define a portion of the lower cavity 3212 or a portion of the upper cavity 3222. The pinch plate 3250 can be disposed within a cavity region defined by the housing cover 3220 or the gasket 3280. The base fluid outlet 3234 and the cap fluid inlet 3236 are in fluid communication via a gasket 3280 and a septum 3260. Alternatively, the base fluid outlet 3234 and the lid fluid inlet 3236 may be fluidly connected on the exterior of the housing base 3210 or housing lid 3220. Septum 3260 provides spacing between lower lumen 3212 and upper lumen 3222. The pinch plate 3250 is disposed within cavities 3212, 3222 defined within the housing cover 3220 and the housing base 3210. The pinch plate 3250 includes pinch points 3252 disposed opposite the pinch structures 3214. A pinch point 3252 with a rounded tip is illustrated. Alternatively, the pinch point 3252 may have a sharp tip. The pinch plate 3250 moves relative to the housing base 3210 to pinch the pinch tube 3240 to restrict fluid flow through the pinch tube 3240 based on fluid pressure within the fluid path 3270 and gas pressure within the lower cavity 3212.

The valves described herein operate to regulate fluid flow as a function of gas pressure within the lower chamber. Fig. 20 illustrates the valve structure before fluid is applied to the valve 3200, and fig. 21-22 illustrate the equilibrium state of the valve in which fluid flows through the valve 3300 at a flow rate based on the input gas pressure. An embodiment of a pinch valve in operation will be described below with reference to fig. 20, 21 and 22.

Gas pressure is applied to the valve's gas inlet 3230, 3330 to pressurize the lower chamber 3212, 3312 at the input/reference gas pressure. The pressurized lower cavity applies an upward force against the pinch plate 3250, 3350 and the diaphragm 3260, 3360 toward the housing cover 3220, 3320. Fluid is applied to the base fluid inlet 3332 and flows sequentially through the clamp tube 3340, the base fluid outlet 3334, the lid fluid inlet 3336, the fluid path 3370, the lid fluid outlet 3338, and then exits the valve. The fluid flowing through the housing cap 3320 exerts a downward force against the diaphragm 3360 and the pinch plate 3350 toward the housing base 3310. As the fluid pressure in the fluid path 3370 increases relative to the gas pressure in the lower chamber 3312, the diaphragm 3360 moves toward the housing base 3310 and exerts a downward force against the pinch plate 3350. In particular, the diaphragm 3360 is to urge the pinch point 3352 relative to the pinch structure 3314 in response to a difference between the pressure of the fluid in the upper chamber 3322 and the pressure of the gas in the lower chamber 3312. For example, the diaphragm 360 is to urge the pinch point 3352 toward the pinch structure 3314 to restrict fluid flow in the pinch tube 3340 in response to an increase in fluid pressure within the upper chamber 3322 relative to gas pressure in the lower chamber 3312.

As the pinch plate 3350 moves toward the housing base 3310, the pinch point 3352 applies a downward force on the pinch tube 3340 so as to pinch the tube 3340 against the pinch structure 3314 and restrict the fluid flow or cause a pressure drop on the pinch tube 3340 and in the upper chamber 3322 until the input gas pressure counteracts the fluid pressure in the upper chamber 3322 to thereafter provide a constant fluid flow rate from the valve 3300. Fig. 22 illustrates the valve 3300, with directional arrows 3380 indicating the fluid flow path through the valve 3300.

The pinching driving force of the diaphragm-driven pinching valve causes the output fluid pressure to be adjusted by the input gas pressure. By setting the pressure in the lower gas chamber 3312 to a known value, the fluid flow and pressure exiting the housing cap 320 is controlled. In this way, the valve self-adjusts to achieve equilibrium and can provide the desired constant fluid flow. In summary, the output fluid pressure at the lid fluid outlet follows the input gas pressure at the gas inlet, and may be independent of the fluid pressure at the substrate fluid inlet.

Fig. 23 and 24 include illustrations of an exemplary sequencing system that includes a manifold 806 to receive a cassette 804. The manifold may be driven up and down using the actuator 808. Optionally, a waste vessel 802 may be positioned within the instrument and fluidly connected to a cartridge 804, for example, as illustrated in the schematic of fig. 2.

As illustrated in fig. 24, a plurality of fluid ports 810 may be connected to tubing and fluid circuits, such as the fluidics schematic illustrated in fig. 2. The cartridge 804 can optionally include an RFID tag readable by the instrument. Connection of the manifold 806 to the cassette 804 can be prevented or permitted based on reading of the RFID tag.

Fig. 25 illustrates another embodiment of a fluidic circuit of the present invention containing five input reactants in a planar circuit configuration. Fig. 25 is a top view of a transparent body or housing 4300 containing a fluid circuit 4302. The housing may be constructed of a variety of materials, including metal, glass, ceramic, plastic, or the like. The transparent material comprises polycarbonate, polymethyl methacrylate, or the like. The inlet (or input port) is connected by a passageway to its corresponding connector aperture (e.g., 4370) on the bottom surface of the housing from which the reactant enters the fluid circuit 4302. The inlet is in fluid communication with a passage (e.g., 4353) which is in turn connected to a curvilinear passage. Each curvilinear path consists of two branches identified for the curvilinear path at "T" junction 4356. One leg is an inner leg connecting its respective inlet to the node (or multi-purpose central port) 4301 and the other leg is an outer leg connecting its respective inlet to the waste passage (or annulus) 4340. As mentioned above, the cross-sectional areas and lengths of the inner and outer legs of the curvilinear passage may be selected to achieve a desired flow balance at the "T" junction and at the node 4301. Via the passage, a waste passage (or channel) 4340 is in fluid communication with a waste port 4345, the waste port 4345 being connected to a waste reservoir (not shown) by a connector slot on the bottom surface of the body. The node 4301 is in fluid communication with the port 4363 through a passage 4361, the passage 4361 being external to the body 4300 in this embodiment and illustrated by a dashed line. In other embodiments, the passages 4361 may be formed in the body such that connector slots for the node 4301 and the port 4363 are not necessary. The port is connected by a passageway 4363 to a cleaning solution inlet (where a "T" junction is formed) and to a connector slit, which in turn provides a conduit to a flow cell, reaction chamber, or the like. Fig. 25 illustrates a mode of dispensing fluid to a flow cell using a fluidic circuit. The mode of operation is implemented by valves 4350 associated with each of the input reactants and with the wash solution. In a first mode of operation (selected reactant valve open, all other reactant valves closed, wash solution valve closed), delivering selected reactants to the flow cell; in a second mode of operation (selected reactant valve open, all other reactant valves closed, wash solution valve open), the fluid circuit is primed to deliver the selected reactant; and in a third mode of operation (all reactant valves closed, wash solution valves open) (not shown), all passages in the fluid circuit are washed. As mentioned above, a valve 4350 is associated with each inlet, and a valve 4350 may be open to allow fluid to enter the fluid circuit 4302 via its respective inlet (as shown for valve 4352) or closed to prevent fluid from entering the circuit 4302 (as shown for all valves, except 4352). In various circumstances, when the valve of the inlet is open and the other valve is closed (including the wash solution valve), as shown for inlet 4370 in fig. 25, fluid flows through passage 4354 to "T" junction 4356 where it splits into two flows, one of which leads to waste passage 4340 and then to waste port 4345, and the other of which leads to node 4301. This second stream is again split from node 4301 into multiple streams, one of which exits node 4301 via pathway 4361 and then reaches pathway 4363 and reaches the flow cell, and the other streams reach each of the pathways connecting node 4301 to the other inlets, and then reach waste pathway 4340 and waste port 4345. The latter stream passes through the other inlet, carrying any material diffused or leaked therefrom and directing it to the waste port 4345. Different sequences of reactants can be directed to the flow cell by opening the valve for the selected reactant and simultaneously closing the valves for all unselected reactants and wash solutions. In one embodiment, this sequence may be implemented by a sequence of operational modes of the fluid circuit, such as: cleaning, priming reactant x1, delivery reactant x1, cleaning, priming reactant x2, delivery reactant x2, cleaning, and the like. For a reactant priming mode, such as a reactant delivery mode, all reactant inlet valves are closed except for the valve corresponding to the selected reactant. However, unlike the reactant delivery mode, the purge solution valve is open, and the relative pressures of the selected reactant stream and the purge solution stream are selected such that the purge solution flows through passage 4361 and enters node 4301 where it then exits through all passages leading to waste passage 4340, except the passage leading to the selected reactant inlet.

As illustrated in fig. 26, a method 900 for preparing a reagent solution within a cartridge includes inserting the cartridge into an instrument, as illustrated at 902. For example, a cartridge may be inserted under the manifold, similar to the embodiment illustrated in fig. 23 or 24, or the instrument illustrated in fig. 1.

Optionally, the system can inspect the cartridge alignment feature, as illustrated at 904. For example, the cartridge may include structure that indicates proper positioning of the cartridge within the instrument. As further illustrated at 906, the cartridge can optionally include a radio frequency identifier tag (RFID tag) that can be read by the instrument. Based on the testing of the cartridge alignment feature or the reading of the RFID tag of the cartridge, the instrument may selectively engage the cartridge using the manifold.

For example, the instrument may connect a plurality of fluid ports secured to the manifold to the cassette, providing fluid connectivity with the rest of the instrument, as illustrated by 908. The instrument may further connect a gas system, such as a compressed air system, to the cartridge, as illustrated at 910. In an example, the connection to the gas system is incorporated within a manifold that connects the fluid port to the reagent cartridge. In particular, the system may be connected to scrubber inlets and outlets and optionally to a cavity defining a space between the reactant enclosures.

The cartridge cavity may be pressurized, as illustrated at 912. The enclosure or reactant enclosure may be evacuated due to pressurization of the cartridge chamber. After the enclosure is evacuated, the cartridge cavity may be further depressurized.

A solution (e.g., a buffer solution) may be applied via the fluid port, as illustrated at 914. In particular, the solution may be applied universally to each of the reactant enclosures. After the solution is applied, the pressure within the cartridge cavity and can then be cycled. This circulation can cause mixing of the reactants within the enclosure, for example, utilizing the mechanisms described above with respect to fig. 4-16.

Fig. 27 illustrates an exemplary method 9204 for performing a measurement of an analyte followed by a cleaning of the system. For example, as illustrated at 922, pressure may be applied to the cartridge cavity, pressurizing the reactant enclosure.

As illustrated at 924, the reactants may be selectively flowed from the reactant enclosures by opening valves connecting the individual reactant enclosures to the fluid circuit. In particular, the reactants may flow in sequential order from selected individual reactant enclosures, optionally separated by a flow of wash solution from a separate vessel.

While the pressure of the cartridge cavity can provide the driving force for the reactants from the reactant enclosure and the individual reactants can be selected by selectively opening the valves associated with the reactant enclosure, the flow rate can be controlled downstream of the fluidic circuit, as illustrated by 926. In particular, the flow may be controlled downstream of the fluid circuit by controlling the flow to the waste container, for example, using a pinch flow regulator.

The system may then be cleaned by applying pressurized air through the cartridge's scrubber (as illustrated by 928) and flowing the pressurized scrubbing air through the fluid circuit 930. The pressurized air may drive fluid from the fluid circuit to the waste container, for example, via a sensor device and a pinch flow regulator. In another example, the pressurized air may drive the reactant fluid back through its associated valve and into the reactant enclosure within the cartridge. In this case, the cartridge cavity may be depressurized, allowing the pressurized air to drive the reactant fluid back into the reactant enclosure.

As illustrated in fig. 28, a method 940 for preparing a reactant cartridge includes attaching a plurality of reactant enclosure enclosures to a cartridge lid, as illustrated at 942. An exemplary method is provided which is shown or described in more detail in the schematic diagrams of fig. 17 and 18. The cartridge lid may be secured to the cartridge base (as illustrated at 944), and a plurality of reagent containers may be inserted into the plurality of enclosures via the cartridge lid (as illustrated at 946).

The system or instrument may be integrated into a process flow for sequencing. For example, the system may be associated with One performing template preparation

Or Ion

The systems are utilized together. Sequencing can be performed using the instrument after template preparation. The instrument may be configured to perform the initial analysis or may outsource the initial analysis and interpretation to a cloud or external server.

The instrument may be configurable. For example, the system may include one or more central processing units, a configurable amount of RAM, a scalable graphics processing unit, and replaceable memory (from 1 to 12 TB). The instrument is configured to receive and perform sequencing using different sequencing chips. In addition, the system may be upgradeable to access an external server for analysis and interpretation of data received from the sequencing chip.

The multiple chips supported by the instrument may also support multiple assays, allowing for different numbers of reads, read lengths, basic outputs, and applications. Thus, the system is versatile and useful in a variety of research fields.

This system is provided for desirable sequencing runs, including outputs from P1 proton chips containing 19.6Gb or high precision runs containing 15.4 Gb.

In a first aspect, a method of preparing a reagent includes inserting a cartridge into an instrument. The cartridge includes a plurality of reagent enclosures disposed in a cavity of the cartridge and exposing the port to an exterior of the cartridge. Each reactant enclosure includes a reactant container containing a reactant and an internal cavity defining a compressible volume, an opening being defined through the reactant container to the internal cavity. The method further comprises: connecting a plurality of fluid ports to openings of the plurality of reactant enclosures; applying a solution via a fluid port to at least partially fill the plurality of reactant enclosures; and a pressure of the circulation chamber, whereby for each of the reactant enclosures, during increasing the pressure, the solution enters the interior chamber of the reactant container, combines with the reactant, and compresses the compressible volume, and during decreasing the pressure, the compressible volume decreases and the reactant is ejected through the opening.

In an example of the first aspect, the method further includes pressurizing the cavity before applying the solution to remove gas from the plurality of enclosures.

In another example of the first aspect and the examples above, the reactant reservoir further comprises a compressible member disposed in the compressible volume.

In another example of the first aspect and the above example, the reactant comprises a nucleotide.

In additional examples of the first aspect and examples above, the method further includes sensing a position of a cartridge prior to connecting the plurality of fluid ports.

In another example of the first aspect and examples above, the method further comprises reading the identification tag of the cartridge with an instrument. For example, the method may further include connecting the plurality of fluidic ports based on the reading.

In another example of the first aspect and examples above, the cartridge further includes a scrubber, the method further comprising connecting a gas system to the scrubber. For example, the scrubber is a CO2 scrubber. In another example, cycling the pressure includes applying a gas through a scrubber and into a cavity.

In a second aspect, a method of detecting an analyte with an instrument includes applying pressure to a cartridge coupled to the instrument. The cartridge includes a plurality of reagent enclosures disposed in a cavity of the cartridge and exposing the port to an exterior of the cartridge. Each reactant enclosure includes a reactant container containing a reactant and an internal cavity defining a compressible volume, an opening being defined through the reactant container to the internal cavity. The method further includes selectively flowing a reactant from a reactant enclosure of the plurality of reactant cartridges from the cartridges, through a fluidic circuit, a sensor, and a pinch flow regulator to a waste container; and controlling flow to the waste container using the pinch flow controller.

In an example of the second aspect, applying pressure to the cartridge includes flowing gas through a scrubber in the cartridge and into a cavity of the cartridge.

In another example of the second aspect and examples above, the sensor includes an ion sensitive field effect transistor.

In another example of the second aspect and the examples above, applying pressure includes compressing air with a compressor of the instrument.

In a third aspect, a method of cleaning an instrument comprises: applying pressurized air through a scrubber of the cartridge; and flowing the washed pressurized air through a fluidic circuit, a portion of the washed pressurized air pushing fluid through the fluidic circuit toward the reagent enclosure of the cartridge and a portion through a pinch flow regulator to a waste container via a sensor of the instrument.

In a fourth aspect, a method for preparing a reagent cartridge comprises: attaching a plurality of enclosure closures to the cartridge lid; securing a cartridge lid to a cartridge base, the cartridge lid defining a plurality of openings, the opening of the cartridge lid providing access to an interior of an enclosure of the plurality of enclosures; and inserting a plurality of reagent containers into the plurality of enclosures, a reagent container of the plurality of reagent containers extending through the opening to an interior of the enclosure, the reagent container comprising a reagent and an interior cavity defining a compressible volume defining access from the reagent container to the interior cavity.

In an example of the fourth aspect, the reagent comprises a nucleotide.

In another example of the fourth aspect and the examples above, the nucleotide is disposed on a porous material within the internal cavity of the reagent container.

In another example of the fourth aspect and examples above, the method further includes inserting the scrubber into the cartridge prior to securing the cartridge lid.

In a fifth aspect, a system comprises: a cartridge manifold to connect to the cartridge and provide fluid communication between the plurality of reactant enclosures and the fluid circuit and between the compressed gas system, the cartridge cavity, and the scrubber of the cartridge; a fluid circuit; a sequencing device in fluid communication with the fluidic circuit; a pinch flow regulator in fluid communication with the sequencing device; and a waste container in fluid communication with the nip flow regulator.

It should be noted that not all of the activities described above in the general description or the examples are required, that a portion of a particular activity may not be required, and that one or more other activities may be performed in addition to those described. Again, the order in which activities are listed is not necessarily the order in which they are performed.

In the foregoing specification, the concepts have been described with reference to specific embodiments. However, one of ordinary skill in the art appreciates that various modifications and changes can be made without departing from the scope of the present invention as set forth in the claims below. Accordingly, the specification and figures are to be regarded in an illustrative rather than a restrictive sense, and all such modifications are intended to be included within the scope of present invention.

As used herein, the terms "comprises," "comprising," "includes," "including," "has," "having" or any other variation thereof, are intended to cover a non-exclusive inclusion. For example, a process, method, article, or apparatus that comprises a list of features is not necessarily limited to only those features but may include other features not expressly listed or inherent to such process, method, article, or apparatus. Additionally, unless expressly stated to the contrary, "or" refers to an inclusive "or" and not to an exclusive "or". For example, condition a or B is satisfied by any one of the following: a is true (or present) and B is false (or not present), a is false (or not present) and B is true (or present), and both a and B are true (or present).

Also, the use of "a" or "an" is used to describe elements and components described herein. This is done merely for convenience and to give a general sense of the scope of the invention. This description should be read to include one or at least one and the singular also includes the plural unless it is obvious that it is meant otherwise.

Benefits, other advantages, and solutions to problems have been described above with regard to specific embodiments. The benefits, advantages, solutions to problems, and any feature(s) that may cause any benefit, advantage, or solution to occur or become more pronounced, however, are not to be construed as a critical, required, or essential feature or feature of any or all the claims.

After reading this specification, skilled artisans will appreciate that certain features are, for clarity, described herein in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features that are, for brevity, described in the context of a single embodiment, may also be provided separately or in any subcombination. Additionally, reference to a value stated in a range includes each value within that range.

Claims (20)

1. A system, comprising:

a case body;

a cartridge manifold to connect to the cartridge and provide fluid communication between a plurality of reactant enclosures of the cartridge and a fluid circuit, and provide fluid communication between a compressed gas system and a cartridge cavity of the cartridge;

the fluid circuit;

a sequencing device in fluid communication with the fluidic circuit;

a sequencing device receiver in fluid communication with the fluidic circuit;

a pinch flow regulator in fluid communication with the sequencing device; and

a waste container in fluid communication with the nip flow regulator.

2. The system of claim 1, wherein each reactant enclosure of the cartridge is in fluid communication with the fluid circuit through a separate fluid connection.

3. The system of claim 2, wherein a single fluid connection connects the fluidic circuit to the sequencing device receiver.

4. The system of claim 1, further comprising a sequencing device disposed in the sequencing device receiver, the sequencing device in fluid communication with the fluidic circuit and the pinch flow regulator.

5. The system of claim 4, wherein the sequencing device comprises a flow cell to receive fluid from the fluidic circuit and provide fluid to the pinch flow regulator.

6. The system of claim 1, further comprising the cartridge, the cartridge comprising:

a tank defining the cartridge cavity and having a gas port for connection to the compressed gas system; and

a plurality of enclosures disposed within the cartridge cavity and secured to the case, each enclosure of the plurality of enclosures comprising:

a fluid port providing a passage for fluid into the interior of the enclosure;

a container disposed within each enclosure, the container defining an internal cavity having a compressible volume and defining a passageway providing fluid communication between the internal cavity and an exterior of the container; and

a reagent disposed within the internal cavity.

7. The system of claim 6, further comprising a compressible member disposed within the internal cavity.

8. The system of claim 7, wherein the compressible member comprises a resilient foam.

9. The system of claim 6, wherein each enclosure of the plurality of enclosures is secured to the container, the container providing fluid access to the fluid port of each enclosure.

10. The system of claim 6, wherein the container is secured to the enclosure by an arm coupling the container to the enclosure.

11. The system of claim 6, wherein the enclosure is a bag enclosure.

12. The system of claim 6, wherein each enclosure further comprises a set of arms coupled to the container to substantially centrally position the container within the enclosure.

13. The system of claim 6, wherein the reagent of each enclosure comprises a unique lyophilized nucleotide, a nucleotide solution, or a pH-adjusted solution.

14. The system of claim 6, wherein the container includes an insert coupled to a fitting to form the internal cavity.

15. The system of claim 6, further comprising a flange coupled to the container and the fluid port.

16. The system of claim 6, wherein the cartridge further comprises a scrubber fluidly coupled between the cartridge cavity and the compressed gas system.

17. The system of claim 16, wherein the scrubber is CO₂A washer.

18. The system of claim 1, further comprising an identification tag attached to the cartridge.

19. The system of claim 18, further comprising a reader that reads the identification tag.

20. The system of claim 1, further comprising a second pinch flow regulator in fluid communication with the fluid circuit and the waste container.

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